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Chen H, Schürch CM, Noble K, Kim K, Krutzik PO, O'Donnell E, Vander Tuig J, Nolan GP, McIlwain DR. Functional comparison of PBMCs isolated by Cell Preparation Tubes (CPT) vs. Lymphoprep Tubes. BMC Immunol 2020; 21:15. [PMID: 32228458 PMCID: PMC7106580 DOI: 10.1186/s12865-020-00345-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 03/12/2020] [Indexed: 11/10/2022] Open
Abstract
Background Cryopreserved human peripheral blood mononuclear cells (PBMCs) are a commonly used sample type for a variety of immunological assays. Many factors can affect the quality of PBMCs, and careful consideration and validation of an appropriate PBMC isolation and cryopreservation method is important for well-designed clinical studies. A major point of divergence in PBMC isolation protocols is the collection of blood, either directly into vacutainers pre-filled with density gradient medium or the use of conical tubes containing a porous barrier to separate the density gradient medium from blood. To address potential differences in sample outcome, we isolated, cryopreserved, and compared PBMCs using parallel protocols differing only in the use of one of two common tube types for isolation. Methods Whole blood was processed in parallel using both Cell Preparation Tubes™ (CPT, BD Biosciences) and Lymphoprep™ Tubes (Axis-Shield) and assessed for yield and viability prior to cryopreservation. After thawing, samples were further examined by flow cytometry for cell yield, cell viability, frequency of 10 cell subsets, and capacity for stimulation-dependent CD4+ and CD8+ T cell intracellular cytokine production. Results No significant differences in cell recovery, viability, frequency of immune cell subsets, or T cell functionality between PBMC samples isolated using CPT or Lymphoprep tubes were identified. Conclusion CPT and Lymphoprep tubes are effective and comparable methods for PBMC isolation for immunological studies.
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Affiliation(s)
- Han Chen
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Christian M Schürch
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | | | | | | | | | | | - Garry P Nolan
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - David R McIlwain
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, USA. .,WCCT Global Inc., Cypress, CA, USA.
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Ding X, Krutzik PO, Ghaffari AA, Zhaozhi Y, Miranda D, Cheng G, Ho CM, Nolan GP, Sanchez DJ. Cellular Signaling Analysis shows antiviral, ribavirin-mediated ribosomal signaling modulation. Antiviral Res 2019; 171:104598. [PMID: 31513822 PMCID: PMC7114107 DOI: 10.1016/j.antiviral.2019.104598] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 09/05/2019] [Accepted: 09/07/2019] [Indexed: 11/17/2022]
Abstract
As antiviral drug resistance develops and new viruses emerge there is a pressing need to develop strategies to rapidly develop antiviral therapeutics. Here we use phospho-specific flow cytometry to assess perturbations of many different cellular signaling pathways during treatment with drug combinations that are highly effective in blocking Herpes simplex virus type 1 (HSV-1) infection. We discovered two antiviral drug combinations act on distinct signaling pathways, either STAT1 or S6 phosphorylation, to block HSV-1 infection. We focused on upregulation of S6 phosphorylation by HSV-1 infection, and our subsequent finding that ribavirin antagonizes this upregulation of S6 phosphorylation. We go on to show that the S6 kinase inhibitor SL0101 blocks HSV-1 replication in vitro and in an in vivo animal model of HSV-1 infection. Overall, we have used an unbiased analysis of cellular signaling pathways during treatment by antiviral drug combinations to discover a novel antiviral drug target against HSV-1 infection. The outcomes of the approach we present highlight the importance of analyzing how antiviral drugs modulate cellular and pathogen-induced signaling as a method to discover new drug therapy targets.
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Affiliation(s)
- Xianting Ding
- Institute for Personalized Medicine, State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, PR China
| | - Peter O Krutzik
- Microbiology & Immunology - Baxter Laboratory, Stanford University, Palo Alto, CA, USA
| | - Amir Ali Ghaffari
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, CA, USA
| | - Yixiu Zhaozhi
- Institute for Personalized Medicine, State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, PR China
| | - Daniel Miranda
- Pharmaceutical Sciences Department, Western University of Health Sciences, Pomona, CA, USA
| | - Genhong Cheng
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, CA, USA
| | - Chih-Ming Ho
- Mechanical and Aerospace Engineering Department, School of Engineering and Applied Science, University of California, Los Angeles, CA, USA
| | - Garry P Nolan
- Microbiology & Immunology - Baxter Laboratory, Stanford University, Palo Alto, CA, USA
| | - David Jesse Sanchez
- Pharmaceutical Sciences Department, Western University of Health Sciences, Pomona, CA, USA.
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O'Donnell EA, Alvendia EL, Osetek BE, Wehrman TS, Krutzik PO. Abstract 2496: Defining the cell surface landscape in cancer: Comprehensive profiling of surface antigens for biomarker discovery and immune monitoring. Cancer Res 2014. [DOI: 10.1158/1538-7445.am2014-2496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Flow cytometric analysis of surface marker expression is a fundamental component of diagnosis, classification, and monitoring for many hematologic malignancies. However, most clinical implementations of surface immunophenotyping focus on only a handful of markers. A comprehensive survey of CD markers and cell-surface receptors could provide a higher resolution and more accurate characterization of cancer lineages, as well as a better understanding of the immune response to disease progression or therapeutic intervention. To this end, we collated and validated 400 antibodies to known markers and receptors. Antibodies were validated for their performance on live and formaldehyde-stabilized samples to ensure compatibility with standard processing procedures. To establish the baseline and variability of each marker in the normal human population, a protocol was established to co-stain each sample for CD3, CD19, CD16, CD56, and CD14 simultaneously with each of the 400 markers. Differences in antigen abundance and expression frequency were calculated to establish the variation inherent in each marker across the population. To further validate the application of this panel for cancer immunophenotyping, eight commonly studied leukemia and lymphoma cell lines were selected for comprehensive surface characterization. Prior to staining, each cell line was fixed and barcoded with a combination of fluorescent dyes to generate a unique fluorescent signature. This approach allowed multiple cell lines to be combined into a single well for staining and analysis, enabling the rapid evaluation of hundreds of surface antigens using less than five million cells from each line. These studies have resulted in the optimization of a protocol and antibody panel for use in profiling surface protein expression on fixed human blood cells and cell lines. Application of this procedure to clinical samples may provide information useful for biomarker discovery, improved stratification of hematologic malignancies, and the identification of new drug targets.
Citation Format: Erika A. O'Donnell, Erica L. Alvendia, Benjamin E. Osetek, Tom S. Wehrman, Peter O. Krutzik. Defining the cell surface landscape in cancer: Comprehensive profiling of surface antigens for biomarker discovery and immune monitoring. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2496. doi:10.1158/1538-7445.AM2014-2496
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Wehrman TS, O'Donnell EA, Lumpe MJ, Osetek BE, Krutzik PO. Abstract 5385: A novel cell-based kinase assay panel paired with high content phenotypic profiling to correlate kinase inhibitor specificity and cellular activity. Cancer Res 2014. [DOI: 10.1158/1538-7445.am2014-5385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
In many cancers, drugs that target a single kinase often lack efficacy due to the presence of alternate oncogenic signaling pathways that may compensate for the inhibition of the targeted kinase. Although completely non-selective kinase inhibitors are highly toxic, selective and simultaneous inhibition of a number of kinases can lead to greater responses. Here we describe the development of a multiplexed cellular kinase assay platform in which compounds are simultaneously profiled against more than 12 kinase targets in a single sample. Using this high-throughput platform, target activity and selectivity in cells can be optimized concurrently, enabling the selection of specific multi-targeted compounds. Using this platform, 300 kinase inhibitors were fully characterized for cellular activity and potency across a large panel of tyrosine kinases. These inhibitors were then tested across a panel of diverse cancer cell lines in a phenotypic screen for their ability to affect viability, cell cycle, and apoptosis under different growth conditions. The resulting comprehensive data set of existing in vitro data, cellular kinase data, and phenotypic screening results provided novel insights into the relationship between inhibitor selectivity, cell cycle effects, and the correlation to anti-cancer activity.
Citation Format: Tom S. Wehrman, Erika A. O'Donnell, M. Jared Lumpe, Benjamin E. Osetek, Peter O. Krutzik. A novel cell-based kinase assay panel paired with high content phenotypic profiling to correlate kinase inhibitor specificity and cellular activity. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5385. doi:10.1158/1538-7445.AM2014-5385
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Abstract
Here we present phospho-specific flow cytometry as a new tool for drug discovery with applications throughout the drug development pipeline, from target identification to library screening, disease model assessment and clinical screening and diagnostics. The single cell, multiparameter nature of flow cytometry generates high-content datasets, and current improvements in the technology are rapidly increasing its high-throughput capacity, making it a valuable platform in modern drug discovery.:
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Affiliation(s)
- Matthew R Clutter
- Baxter Laboratory of Genetic Pharmacology, Department of Microbiology and Immunology, School of Medicine, Stanford University, 269 Campus Drive, CCSR 3205, Stanford, CA 94305, USA
| | - Peter O Krutzik
- Baxter Laboratory of Genetic Pharmacology, Department of Microbiology and Immunology, School of Medicine, Stanford University, 269 Campus Drive, CCSR 3205, Stanford, CA 94305, USA
| | - Garry P Nolan
- Baxter Laboratory of Genetic Pharmacology, Department of Microbiology and Immunology, School of Medicine, Stanford University, 269 Campus Drive, CCSR 3205, Stanford, CA 94305, USA.
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Kinoshita SM, Krutzik PO, Nolan GP. COP9 signalosome component JAB1/CSN5 is necessary for T cell signaling through LFA-1 and HIV-1 replication. PLoS One 2012; 7:e41725. [PMID: 22911848 PMCID: PMC3404009 DOI: 10.1371/journal.pone.0041725] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Accepted: 06/25/2012] [Indexed: 02/01/2023] Open
Abstract
To determine critical host factors involved in HIV-1 replication, a dominant effector genetics approach was developed to reveal signaling pathways on which HIV-1 depends for replication. A large library of short peptide aptamers was expressed via retroviral delivery in T cells. Peptides that interfered with T cell activation-dependent processes that might support HIV-1 replication were identified. One of the selected peptides altered signaling, lead to a difference in T cell activation status, and inhibited HIV-1 replication. The target of the peptide was JAB1/CSN5, a component of the signalosome complex. JAB1 expression overcame the inhibition of HIV-1 replication in the presence of peptide and also promoted HIV-1 replication in activated primary CD4+ T cells. This peptide blocked physiological release of JAB1 from the accessory T cell surface protein LFA-1, downstream AP-1 dependent events, NFAT activation, and HIV-1 replication. Thus, genetic selection for intracellular aptamer inhibitors of host cell processes proximal to signals at the immunological synapse of T cells can define unique mechanisms important to HIV-1 replication.
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Affiliation(s)
- Shigemi M Kinoshita
- Laboratory of Immune Regulation, Osaka University Graduate School of Frontier Biosciences, Suita, Osaka, Japan.
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Abstract
This protocol describes methods for monitoring intracellular phosphorylation-dependent signaling events on a single-cell basis. This approach measures cell signaling by treating cells with exogenous stimuli, fixing cells with formaldehyde, permeabilizing with methanol, and then staining with phospho-specific antibodies. Thus, cell signaling states can be determined as a measure of how cells interact with their environment. This method has applications in clinical research as well as mechanistic studies of basic biology. In clinical research, diagnostic or drug efficacy information can be retrieved by discovering how a disease affects the ability of cells to respond to growth factors. Basic scientists can use this technique to analyze signaling events in cell lines and human or murine primary cells, including rare populations, like B1 cells or stem cells. This technique has broad applications bringing standard biochemical analysis into primary cells in order to garner valuable information about signaling events in physiologic settings.
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Thomas C, Moraga I, Levin D, Krutzik PO, Podoplelova Y, Trejo A, Lee C, Yarden G, Vleck SE, Glenn JS, Nolan GP, Piehler J, Schreiber G, Garcia KC. Structural linkage between ligand discrimination and receptor activation by type I interferons. Cell 2011; 146:621-32. [PMID: 21854986 PMCID: PMC3166218 DOI: 10.1016/j.cell.2011.06.048] [Citation(s) in RCA: 259] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2011] [Revised: 05/17/2011] [Accepted: 06/15/2011] [Indexed: 11/16/2022]
Abstract
Type I Interferons (IFNs) are important cytokines for innate immunity against viruses and cancer. Sixteen human type I IFN variants signal through the same cell-surface receptors, IFNAR1 and IFNAR2, yet they can evoke markedly different physiological effects. The crystal structures of two human type I IFN ternary signaling complexes containing IFNα2 and IFNω reveal recognition modes and heterotrimeric architectures that are unique among the cytokine receptor superfamily but conserved between different type I IFNs. Receptor-ligand cross-reactivity is enabled by conserved receptor-ligand "anchor points" interspersed among ligand-specific interactions that "tune" the relative IFN-binding affinities, in an apparent extracellular "ligand proofreading" mechanism that modulates biological activity. Functional differences between IFNs are linked to their respective receptor recognition chemistries, in concert with a ligand-induced conformational change in IFNAR1, that collectively control signal initiation and complex stability, ultimately regulating differential STAT phosphorylation profiles, receptor internalization rates, and downstream gene expression patterns.
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Affiliation(s)
- Christoph Thomas
- Howard Hughes Medical Institute, Departments of Molecular and Cellular Physiology, and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ignacio Moraga
- Howard Hughes Medical Institute, Departments of Molecular and Cellular Physiology, and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Doron Levin
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Peter O. Krutzik
- Department of Microbiology and Immunology, Baxter Lab in Stem Cell Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yulia Podoplelova
- Division of Biophysics, University of Osnabrück, 49076 Osnabrück, Germany
| | - Angelica Trejo
- Department of Microbiology and Immunology, Baxter Lab in Stem Cell Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Choongho Lee
- Department of Medicine, Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ganit Yarden
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Susan E. Vleck
- Department of Medicine, Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jeffrey S. Glenn
- Department of Medicine, Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Garry P. Nolan
- Department of Microbiology and Immunology, Baxter Lab in Stem Cell Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jacob Piehler
- Division of Biophysics, University of Osnabrück, 49076 Osnabrück, Germany
| | - Gideon Schreiber
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - K. Christopher Garcia
- Howard Hughes Medical Institute, Departments of Molecular and Cellular Physiology, and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
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9
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Bendall SC, Simonds EF, Qiu P, Amir EAD, Krutzik PO, Finck R, Bruggner RV, Melamed R, Trejo A, Ornatsky OI, Balderas RS, Plevritis SK, Sachs K, Pe'er D, Tanner SD, Nolan GP. Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum. Science 2011; 332:687-96. [PMID: 21551058 DOI: 10.1126/science.1198704] [Citation(s) in RCA: 1664] [Impact Index Per Article: 128.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Flow cytometry is an essential tool for dissecting the functional complexity of hematopoiesis. We used single-cell "mass cytometry" to examine healthy human bone marrow, measuring 34 parameters simultaneously in single cells (binding of 31 antibodies, viability, DNA content, and relative cell size). The signaling behavior of cell subsets spanning a defined hematopoietic hierarchy was monitored with 18 simultaneous markers of functional signaling states perturbed by a set of ex vivo stimuli and inhibitors. The data set allowed for an algorithmically driven assembly of related cell types defined by surface antigen expression, providing a superimposable map of cell signaling responses in combination with drug inhibition. Visualized in this manner, the analysis revealed previously unappreciated instances of both precise signaling responses that were bounded within conventionally defined cell subsets and more continuous phosphorylation responses that crossed cell population boundaries in unexpected manners yet tracked closely with cellular phenotype. Collectively, such single-cell analyses provide system-wide views of immune signaling in healthy human hematopoiesis, against which drug action and disease can be compared for mechanistic studies and pharmacologic intervention.
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Affiliation(s)
- Sean C Bendall
- Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
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Abstract
Fluorescent cell barcoding (FCB) enables high throughput, high content flow cytometry by multiplexing samples prior to staining and acquisition on the cytometer. Individual cell samples are barcoded, or labeled, with unique signatures of fluorescent dyes so that they can be mixed together, stained, and analyzed as a single sample. By mixing samples prior to staining, antibody consumption is typically reduced 10- to 100-fold. In addition, data robustness is increased through the combination of control and treated samples, which minimizes pipetting error, staining variation, and the need for normalization. Finally, speed of acquisition is enhanced, enabling large profiling experiments to be run with standard cytometer hardware. In this unit, we outline the steps necessary to apply the FCB method to cell lines, as well as primary peripheral blood samples. Important technical considerations, such as choice of barcoding dyes, concentrations, labeling buffers, compensation, and software analysis, are discussed.
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Affiliation(s)
- Peter O Krutzik
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, California, USA
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11
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Clutter MR, Heffner GC, Krutzik PO, Sachen KL, Nolan GP. Tyramide signal amplification for analysis of kinase activity by intracellular flow cytometry. Cytometry A 2011; 77:1020-31. [PMID: 20824632 DOI: 10.1002/cyto.a.20970] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Intracellular flow cytometry permits quantitation of diverse molecular targets at the single-cell level. However, limitations in detection sensitivity inherently restrict the method, sometimes resulting in the inability to measure proteins of very low abundance or to differentiate cells expressing subtly different protein concentrations. To improve these measurements, an enzymatic amplification approach called tyramide signal amplification (TSA) was optimized for assessment of intracellular kinase cascades. First, Pacific Blue, Pacific Orange, and Alexa Fluor 488 tyramide reporters were shown to exhibit low nonspecific binding in permeabilized cells. Next, the effects of antibody concentration, tyramide concentration, and reaction time on assay resolution were characterized. Use of optimized TSA resulted in a 10-fold or greater improvement in measurement resolution of endogenous Erk and Stat cell signaling pathways relative to standard, nonamplified detection. TSA also enhanced assay sensitivity and, in conjunction with fluorescent cell barcoding, improved assay performance according to a metric used to evaluate high-throughput drug screens. TSA was used to profile Stat1 phosphorylation in primary immune system cells, which revealed heterogeneity in various populations, including CD4+ FoxP3+ regulatory T cells. We anticipate the approach will be broadly applicable to intracellular flow cytometry assays with low signal-to-noise ratios.
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Affiliation(s)
- Matthew R Clutter
- Department of Microbiology and Immunology, Baxter Laboratory for Stem Cell Biology, Stanford University School of Medicine, Stanford, California, USA
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12
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Krutzik PO, Trejo A, Schulz KR, Nolan GP. Phospho flow cytometry methods for the analysis of kinase signaling in cell lines and primary human blood samples. Methods Mol Biol 2011; 699:179-202. [PMID: 21116984 DOI: 10.1007/978-1-61737-950-5_9] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Phospho-specific flow cytometry, or phospho flow, measures the phosphorylation state of intracellular proteins at the single cell level. Many phosphorylation events can be analyzed simultaneously in each cell, along with cell surface markers, enabling complex biochemical signaling networks to be resolved in heterogeneous cell populations. The method has been applied to many diverse areas of biology, including the characterization of signaling pathways in normal immune responses to antigenic stimulation and microbial challenge, alteration of signaling networks that occur in cancer and autoimmune diseases, and high-throughput, high-content drug discovery. In this chapter, we provide detailed experimental protocols for performing phospho flow in cell lines, Ficoll-purified peripheral blood mononuclear cells, and whole blood. These protocols are applicable to both human and murine samples. We also provide methods for the validation of surface marker antibodies for use in phospho flow. Finally, we discuss data analysis methods, in particular, how to quantify changes in phosphorylation and how to visualize the large data sets that can result from experiments in primary cells.
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Affiliation(s)
- Peter O Krutzik
- Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
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O'Gorman WE, Sampath P, Simonds EF, Sikorski R, O'Malley M, Krutzik PO, Chen H, Panchanathan V, Chaudhri G, Karupiah G, Lewis DB, Thorne SH, Nolan GP. Alternate mechanisms of initial pattern recognition drive differential immune responses to related poxviruses. Cell Host Microbe 2010; 8:174-85. [PMID: 20709294 DOI: 10.1016/j.chom.2010.07.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2009] [Revised: 02/26/2010] [Accepted: 06/15/2010] [Indexed: 12/25/2022]
Abstract
Vaccinia immunization was pivotal to successful smallpox eradication. However, the early immune responses that distinguish poxvirus immunization from pathogenic infection remain unknown. To address this, we developed a strategy to map the activation of key signaling networks in vivo and applied this approach to define and compare the earliest signaling events elicited by immunizing (vaccinia) and lethal (ectromelia) poxvirus infections in mice. Vaccinia induced rapid TLR2-dependent responses, leading to IL-6 production, which then initiated STAT3 signaling in dendritic and T cells. In contrast, ectromelia did not induce TLR2 activation, and profound mouse strain-dependent responses were observed. In resistant C57BL/6 mice, the STAT1 and STAT3 pathways were rapidly activated, whereas in susceptible BALB/c mice, IL-6-dependent STAT3 activation did not occur. These data link early immune signaling events to infection outcome and suggest that activation of different pattern-recognition receptors early after infection may be important in determining vaccine efficacy.
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Affiliation(s)
- William E O'Gorman
- Department of Microbiology and Immunology, Baxter Lab in Genetic Pharmacology, Stanford University School of Medicine, Stanford, CA 94305, USA
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Abstract
Cytobank is a Web-based application for storage, analysis, and sharing of flow cytometry experiments. Researchers use a Web browser to log in and use a wide range of tools developed for basic and advanced flow cytometry. In addition to providing access to standard cytometry tools from any computer, Cytobank creates a platform and community for developing new analysis and publication tools. Figure layouts created on Cytobank are designed to allow transparent access to the underlying experiment annotation and data processing steps. Since all flow cytometry files and analysis data are stored on a central server, experiments and figures can be viewed or edited by anyone with the proper permission, from any computer with Internet access. Once a primary researcher has performed the initial analysis of the data, collaborators can engage in experiment analysis and make their own figure layouts using the gated, compensated experiment files. Cytobank is available to the scientific community at http://www.cytobank.org.
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Affiliation(s)
- Nikesh Kotecha
- Stanford University School of Medicine, Stanford, California
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Hale MB, Krutzik PO, Samra SS, Crane JM, Nolan GP. Stage dependent aberrant regulation of cytokine-STAT signaling in murine systemic lupus erythematosus. PLoS One 2009; 4:e6756. [PMID: 19707593 PMCID: PMC2727051 DOI: 10.1371/journal.pone.0006756] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2009] [Accepted: 07/21/2009] [Indexed: 02/07/2023] Open
Abstract
Systemic lupus erythematosus (SLE) is a complex autoimmune disease of unknown etiology that involves multiple interacting cell types driven by numerous cytokines and autoimmune epitopes. Although the initiating events leading to SLE pathology are not understood, there is a growing realization that dysregulated cytokine action on immune cells plays an important role in promoting the inflammatory autoimmune state. We applied phospho-specific flow cytometry to characterize the extent to which regulation of cytokine signal transduction through the STAT family of transcription factors is disturbed during the progression of SLE. Using a panel of 10 cytokines thought to have causal roles in the disease, we measured signaling responses at the single-cell level in five immune cell types from the MRLlpr murine model. This generated a highly multiplexed view of how cytokine stimuli are processed by intracellular signaling networks in adaptive and innate immune cells during different stages of SLE pathogenesis. We report that robust changes in cytokine signal transduction occur during the progression of SLE in multiple immune cell subtypes including increased T cell responsiveness to IL-10 and ablation of Stat1 responses to IFNalpha, IFNgamma, IL-6, and IL-21, Stat3 responses to IL-6, Stat5 responses to IL-15, and Stat6 responses to IL-4. We found increased intracellular expression of Suppressor of Cytokine Signaling 1 protein correlated with negative regulation of Stat1 responses to inflammatory cytokines. The results provide evidence of negative feedback regulation opposing inflammatory cytokines that have self-sustaining activities and suggest a cytokine-driven oscillator circuit may drive the periodic disease activity observed in many SLE patients.
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Affiliation(s)
- Matthew B. Hale
- The Baxter Laboratory of Genetic Pharmacology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Peter O. Krutzik
- The Baxter Laboratory of Genetic Pharmacology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Shamsher S. Samra
- The Baxter Laboratory of Genetic Pharmacology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Janelle M. Crane
- The Baxter Laboratory of Genetic Pharmacology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Garry P. Nolan
- The Baxter Laboratory of Genetic Pharmacology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail:
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O'Gorman WE, Dooms H, Thorne SH, Kuswanto WF, Simonds EF, Krutzik PO, Nolan GP, Abbas AK. The initial phase of an immune response functions to activate regulatory T cells. J Immunol 2009; 183:332-9. [PMID: 19542444 DOI: 10.4049/jimmunol.0900691] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
An early reaction of CD4(+) T lymphocytes to Ag is the production of cytokines, notably IL-2. To detect cytokine-dependent responses, naive Ag-specific T cells were stimulated in vivo and the presence of phosphorylated STAT5 molecules was used to identify the cell populations responding to IL-2. Within hours of T cell priming, IL-2-dependent STAT5 phosphorylation occurred primarily in Foxp3(+) regulatory T cells. In contrast, the Ag-specific T cells received STAT5 signals only after repeated Ag exposure or memory differentiation. Regulatory T cells receiving IL-2 signals proliferated and developed enhanced suppressive activity. These results indicate that one of the earliest events in a T cell response is the activation of endogenous regulatory cells, potentially to prevent autoimmunity.
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Affiliation(s)
- William E O'Gorman
- Department of Microbiology and Immunology, Stanford University School of Medicine, CA 94305, USA
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Hammer MM, Kotecha N, Irish JM, Nolan GP, Krutzik PO. WebFlow: a software package for high-throughput analysis of flow cytometry data. Assay Drug Dev Technol 2009; 7:44-55. [PMID: 19187010 DOI: 10.1089/adt.2008.174] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Flow cytometry has emerged as a powerful tool for quantitative, single-cell analysis of both surface markers and intracellular antigens, including phosphoproteins and kinase signaling cascades, with the flexibility to process hundreds of samples in multiwell plate format. Quantitative flow cytometric analysis is being applied in many areas of biology, from the study of immunology in animal models or human patients to high-content drug screening of pharmacologically active compounds. However, these experiments generate thousands of data points per sample, each with multiple measured parameters, leading to data management and analysis challenges. We developed WebFlow (http://webflow.stanford.edu), a web server-based software package to manage, analyze, and visualize data from flow cytometry experiments. WebFlow is accessible via standard web browsers and does not require users to install software on their personal computers. The software enables plate-based annotation of large data sets, which provides the basis for exploratory data analysis tools and rapid visualization of multiple different parameters. These tools include custom user-defined statistics to normalize data to other wells or other channels, as well as interactive, user-selectable heat maps for viewing the underlying single-cell data. The web-based approach of WebFlow allows for sharing of data with collaborators or the general public. WebFlow provides a novel platform for quantitative analysis of flow cytometric data from high-throughput drug screening or disease profiling experiments.
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Affiliation(s)
- Mark M Hammer
- Baxter Laboratory in Genetic Pharmacology, Department of Microbiology, Stanford University, Stanford, California 94305, USA
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18
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Abstract
This protocol describes methods for monitoring intracellular phosphorylation-dependent signaling events on a single-cell basis. This approach measures cell signaling by treating cells with exogenous stimuli, fixing cells with formaldehyde, permeabilizing with methanol, and then staining with phospho-specific antibodies. Thus, cell signaling states can be determined as a measure of how cells interact with their environment. This method has applications in clinical research as well as mechanistic studies of basic biology. In clinical research, diagnostic or drug efficacy information can be retrieved by discovering how a disease affects the ability of cells to respond to growth factors. Basic scientists can use this technique to analyze signaling events in cell lines and human or murine primary cells, including rare populations, like B1 cells or stem cells. This technique has broad applications to take standard biochemical analysis into primary cells to garner valuable information about signaling events in physiologic settings.
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Krutzik PO, Nolan GP. Fluorescent cell barcoding in flow cytometry allows high-throughput drug screening and signaling profiling. Nat Methods 2006; 3:361-8. [PMID: 16628206 DOI: 10.1038/nmeth872] [Citation(s) in RCA: 429] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2006] [Accepted: 03/10/2006] [Indexed: 11/08/2022]
Abstract
Flow cytometry allows high-content, multiparameter analysis of single cells, making it a promising tool for drug discovery and profiling of intracellular signaling. To add high-throughput capacity to flow cytometry, we developed a cell-based multiplexing technique called fluorescent cell barcoding (FCB). In FCB, each sample is labeled with a different signature, or barcode, of fluorescence intensity and emission wavelengths, and mixed with other samples before antibody staining and analysis by flow cytometry. Using three FCB fluorophores, we were able to barcode and combine entire 96-well plates, reducing antibody consumption 100-fold and acquisition time to 5-15 min per plate. Using FCB and phospho-specific flow cytometry, we screened a small-molecule library for inhibitors of T cell-receptor and cytokine signaling, simultaneously determining compound efficacy and selectivity. We also analyzed IFN-gamma signaling in multiple cell types from primary mouse splenocytes, revealing differences in sensitivity and kinetics between B cells, CD4+ and CD4- T cells and CD11b-hi cells.
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Affiliation(s)
- Peter O Krutzik
- Department of Microbiology and Immunology, Baxter Laboratory in Genetic Pharmacology, Stanford University, Stanford, California 94305, USA
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Wehrman TS, von Degenfeld G, Krutzik PO, Nolan GP, Blau HM. Luminescent imaging of β-galactosidase activity in living subjects using sequential reporter-enzyme luminescence. Nat Methods 2006; 3:295-301. [PMID: 16554835 DOI: 10.1038/nmeth868] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2005] [Accepted: 02/17/2006] [Indexed: 02/06/2023]
Abstract
We generated a sequential reporter-enzyme luminescence (SRL) technology for in vivo detection of beta-galactosidase (beta-gal) activity. The substrate, a caged D-luciferin-galactoside conjugate, must first be cleaved by beta-gal before it can be catalyzed by firefly luciferase (FLuc) to generate light. As a result, luminescence is dependent on beta-gal activity. Using this technology, constitutive beta-gal activity in engineered cells and inducible tissue-specific beta-gal expression in transgenic mice can now be visualized noninvasively over time. A substantial advantage of beta-gal as a bioluminescent probe is that the enzyme retains full activity outside of cells, unlike FLuc, which requires intracellular cofactors. As a result, antibodies conjugated to the recombinant beta-gal enzyme can be used to detect endogenous cells and extracellular antigens in vivo. Thus, coupling the properties of FLuc to the advantages of beta-gal permits bioluminescent imaging applications that previously were not possible.
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Affiliation(s)
- Thomas S Wehrman
- Baxter Laboratory in Genetic Pharmacology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
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Abstract
The immune system is a multitiered network that at the first level uses changes to intracellular signaling proteins to commit cells to determined fates. At the second tier, cells interact with one another via specifically expressed surface receptors and their cognate signaling molecules. At the third level, the local environments of immune cells change the outcomes of intracellular signaling pathways and thereby the role of cells during immune challenge. The interplay among these three tiers allows the distinct cell types of the immune system to respond cohesively to eliminate foreign Ags. In this study, using phosphospecific flow cytometry, we analyze elements of these network tiers by generating profiles of single-cell phosphoprotein responses in B cells, T cells, and myeloid cells to a number of mechanistically and clinically relevant cytokines (IFN-gamma, GM-CSF, IL-2, and IL-10) as well as LPS at key regulatory interfaces (Jak-Stat and MAPK pathways). The stimuli typically induced phosphorylation of specific signaling pathways and exerted their effects on distinct subsets of immune cells. However, upon comparison of stimulation in vitro and in vivo, we noted that signaling pathway specificity and cell type specificity were influenced strongly by the external environment. When taken from the in vivo environment, certain cell subsets became hypo- or hyper-responsive, showed profound differences in sensitivity to cytokine levels, or displayed altered phosphorylation kinetics. Thus, simultaneous analysis of the three tiers of the immune system network illustrates the principles by which immune regulation is context dependent and how in vitro culture systems compare with the in vivo environment.
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Affiliation(s)
- Peter O Krutzik
- Department of Microbiology and Immunology, Baxter Laboratory of Genetic Pharmacology, Stanford University, Stanford, CA 94305, USA
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Krutzik PO, Clutter MR, Nolan GP. Coordinate analysis of murine immune cell surface markers and intracellular phosphoproteins by flow cytometry. J Immunol 2005; 175:2357-65. [PMID: 16081806 DOI: 10.4049/jimmunol.175.4.2357] [Citation(s) in RCA: 108] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Recently, phosphospecific flow cytometry has emerged as a powerful tool to analyze intracellular signaling events in complex populations of cells because of its ability to simultaneously discriminate cell types based on surface marker expression and measure levels of intracellular phosphoproteins. This has provided novel insights into the cell- and pathway-specific nature of immune signaling. However, we and others have found that the fixation and permeabilization steps necessary for phosphoprotein analysis often negatively affect the resolution of cell types based on surface marker analysis and light scatter characteristics. Therefore, we performed a comprehensive profile of >35 different murine surface marker Abs to understand the effects of fixation and permeabilization on surface Ag staining. Fortuitously, approximately 80% of the Abs tested resolved cell populations of interest, although with decreased separation between positive and negative populations and at very different titers than those used on live cells. The other 20% showed either complete loss of separation between populations or loss of intermediately staining populations. We were able to rescue staining of several of these Ags by performing staining after fixation, but before permeabilization, although with limited fluorophore choices. Scatter characteristics of lymphocytes were well retained, but changed dramatically for monocyte and neutrophil populations. These results compile a comprehensive resource for researchers interested in applying phosphospecific flow cytometry to complex populations of cells while outlining steps necessary to successfully apply new surface marker Abs to this platform.
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Affiliation(s)
- Peter O Krutzik
- Department of Microbiology and Immunology, Baxter Laboratory of Genetic Pharmacology, Stanford University, Stanford, CA 94305, USA
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Irish JM, Hovland R, Krutzik PO, Perez OD, Bruserud O, Gjertsen BT, Nolan GP. Potentiated phospho-protein networks in cancer cells. Breast Cancer Res 2005. [PMCID: PMC4233615 DOI: 10.1186/bcr1194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Irish JM, Hovland R, Krutzik PO, Perez OD, Bruserud Ø, Gjertsen BT, Nolan GP. Single cell profiling of potentiated phospho-protein networks in cancer cells. Cell 2004; 118:217-28. [PMID: 15260991 DOI: 10.1016/j.cell.2004.06.028] [Citation(s) in RCA: 542] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2004] [Revised: 05/28/2004] [Accepted: 05/28/2004] [Indexed: 01/28/2023]
Abstract
Altered growth factor responses in phospho-protein-driven signaling networks are crucial to cancer cell survival and pathology. Profiles of cancer cell signaling networks might therefore identify mechanisms by which such cells interpret environmental cues for continued growth. Using multiparameter flow cytometry, we monitored phospho-protein responses to environmental cues in acute myeloid leukemia at the single cell level. By exposing cancer cell signaling networks to potentiating inputs, rather than relying upon the basal levels of protein phosphorylation alone, we could discern unique cancer network profiles that correlated with genetics and disease outcome. Strikingly, individual cancers manifested multiple cell subsets with unique network profiles, reflecting cancer heterogeneity at the level of signaling response. The results revealed a dramatic remodeling of signaling networks in cancer cells. Thus, single cell measurements of phospho-protein responses reveal shifts in signaling potential of a phospho-protein network, allowing for categorizing of cell network phenotypes by multidimensional molecular profiles of signaling.
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Affiliation(s)
- Jonathan M Irish
- Department of Microbiology & Immunology, Baxter Laboratory of Genetic Pharmacology, Stanford University, Stanford, CA 94305, USA
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Abstract
Flow cytometry offers the capability to assess the heterogeneity of cellular subsets that exist in complex populations, such as peripheral blood, based on immunophenotypes. We describe methodologies to measure phospho-epitopes in single cells as determinants of intracellular kinase activity. Multiparametric staining, using both surface and intracellular stains, allows for the study of discrete biochemical events in readily discernible lymphocyte subsets. As such, the usage of multiparameter flow cytometry to obtain proteomic information provides several major advantages: (1) the ability to perform multiparametric experiments to identify distinct signaling profiles in defined lymphocyte populations, (2) simultaneous correlation of multiple active kinases involved in signaling cascades, (3) profiling of active kinase states to identify signaling signatures of interest rapidly, and (4) biochemical access to rare cell subsets such as those from clinically derived samples or populations that comprise too few in numbers for conventional biochemical analysis.
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Affiliation(s)
- Omar D Perez
- The Baxter Laboratory for Genetic Pharmacology, Department of Microbiologyand Immunology, Stanford University School of Medicine, Stanford, CA, USA
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Krutzik PO, Irish JM, Nolan GP, Perez OD. Analysis of protein phosphorylation and cellular signaling events by flow cytometry: techniques and clinical applications. Clin Immunol 2004; 110:206-21. [PMID: 15047199 DOI: 10.1016/j.clim.2003.11.009] [Citation(s) in RCA: 264] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2003] [Accepted: 11/10/2003] [Indexed: 01/16/2023]
Abstract
Analysis of protein phosphorylation with flow cytometric techniques has emerged as a powerful tool in the field of immunological signaling, allowing cellular subsets in complex populations to be analyzed accurately and rapidly. In this review, we examine the development of phospho-epitope, or phospho-specific, flow cytometry and the premises upon which the technique is based. Phospho-specific flow cytometry is compared to traditional biochemical methods, and its advantages, such as single cell analysis, multiparameter data acquisition, rapid protocols, and the ability to analyze rare cell subsets, are detailed. We also discuss the many technical considerations that must be addressed when developing new antibodies or analyzing new epitopes including antigen accessibility, stability of the phospho-epitope, fluorophore selection, surface phenotype integrity, and antibody suitability for staining epitopes inside fixed and permeabilized cells. The methods that have been used to date are described in light of these technical considerations. The importance of developing bioinformatic platforms in parallel with these techniques is emphasized due to the large, multiparameter datasets that are rapidly accumulated and which require more efficient data viewing and complex clustering methods than currently available for flow cytometric data. Finally, we discuss the potential clinical applications of phospho-specific flow cytometry in analyzing immune cell development and antigen-specific immune responses, as well as pharmacodynamic profiling of disease states or drug efficacy and specificity against particular signaling proteins.
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Affiliation(s)
- Peter O Krutzik
- Department of Molecular Pharmacology, School of Medicine, Stanford University, CA 94305, USA
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Abstract
BACKGROUND Recent advances in intracellular staining techniques, cytometer technology, fluorescent reagents, and antibody production have expanded the number of intracellular antigens that can be analyzed by flow cytometry. Measurement of protein phosphorylation with phospho-specific antibodies has given insight into kinase signaling cascades. However, available techniques for phospho-epitope staining can differ greatly, making it necessary to understand the differences between the outcomes when such techniques are applied and to develop robust and reproducible methods of application. METHODS Ten different cellular fixation and permeabilization techniques were tested for their ability to provide phospho-specific staining. Combinations of formaldehyde, methanol, ethanol, acetone, Triton X-100, and saponin were used as fixation and permeabilization reagents. Phospho-specific antibodies were labeled with Alexa Fluor dyes to provide multicolor analysis of different signaling events simultaneously within individual cells. RESULTS Fixing cells with 1.5% formaldehyde followed by permeabilization in methanol gave optimal results for pERK, pp38, pJNK, pStat1, pStat5, and pStat6 staining. Alteration of formaldehyde fixation and methanol permeabilization times affected measurements of phosphorylation induction. Phospho-specific flow cytometric analyses correlated well with Western blotting, providing cross platform validation of the technique. CONCLUSIONS Measuring phosphorylation events by flow cytometry provides a rapid and efficient way to measure kinase cascades in individual cells. Stability of phospho-epitopes in methanol allows long-term storage of samples prior to analysis. Multiple signaling cascades can be monitored simultaneously through the use of different fluorophore labels to determine specificity of ligands or inhibitors. Application of optimized techniques to heterogeneous cell types such as peripheral blood or murine splenocytes may allow signaling to be analyzed simultaneously in immune cell subsets.
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Affiliation(s)
- Peter O Krutzik
- Department of Molecular Pharmacology, School of Medicine, Stanford University, Stanford, California 94305, USA
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Krutzik PO, Chamberlin AR. Synthesis of DNA-binding polyamides. Robust solid-phase methods for coupling heterocyclic aromatic amino acids. Methods Mol Biol 2003; 201:77-92. [PMID: 12357940 DOI: 10.1385/1-59259-285-6:77] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
Affiliation(s)
- Peter O Krutzik
- Department of Chemistry, University of California-Irvine, Irvine, CA, USA
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Abstract
Pyrrole-imidazole polyamides can be synthesized to target predetermined sequences of DNA with nanomolar affinity and high specificity, and have been shown to modulate gene transcription both in vitro and in vivo. To make polyamides more readily available to biological laboratories, we have developed a rapid solid-phase synthesis based on azabenzotriazole (OAt) activation that decreases synthesis time 60% compared to standard benzotriazole (OBt) techniques, without loss of yield or purity.
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Affiliation(s)
- Peter O Krutzik
- Department of Chemistry, University of California-Irvine, CA 92697, Irvine, USA
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Phillips D, Sonnenberg J, Arai AC, Vaswani R, Krutzik PO, Kleisli T, Kessler M, Granger R, Lynch G, Richard Chamberlin A. 5'-alkyl-benzothiadiazides: a new subgroup of AMPA receptor modulators with improved affinity. Bioorg Med Chem 2002; 10:1229-48. [PMID: 11886787 DOI: 10.1016/s0968-0896(01)00405-9] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
AMPA receptors form a major subdivision of the glutamate receptor family that mediates excitatory synaptic transmission in the brain. Currents through AMPA receptors can be up- or down-regulated by compounds that allosterically modulate receptor kinetics through binding sites distinct from that for glutamate. One of those modulators is the benzothiadiazide IDRA-21 which has been reported to enhance synaptic transmission and be effective in behavioral tests, but typically requires threshold concentrations of at least 100 microM to be active in vitro. In this study, new benzothiadiazides were developed with IDRA-21 as lead compound and examined for their potency in modulating AMPA receptor kinetics. A significant increase in drug affinity was obtained by alkyl substitution at the 5'-position of IDRA-21; substitutions at other positions of the benzothiadiazide core generally did not yield a further gain in affinity and in some cases abolished drug binding. The 5'-ethyl derivative exhibited an EC(50) value in the order of 22 microM which represents about a 30-fold gain in affinity over that of IDRA-21. The EC(50) value is comparable to that of cyclothiazide, the most potent benzothiadiazide drug, but the effects on AMPA receptors differed substantially between these two compounds in that the 5'-ethyl derivative of IDRA-21 greatly increased the binding affinity for receptor agonists whereas cyclothiazide is known to reduce agonist binding. The structure--activity relationships reported here thus offer to provide new insights how receptor kinetics is linked to particular aspects of receptor--drug interactions.
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Affiliation(s)
- Dean Phillips
- Department of Chemistry, University of California, Irvine, CA 92697, USA
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Lew A, Krutzik PO, Hart ME, Chamberlin AR. Increasing rates of reaction: microwave-assisted organic synthesis for combinatorial chemistry. J Comb Chem 2002; 4:95-105. [PMID: 11886281 DOI: 10.1021/cc010048o] [Citation(s) in RCA: 285] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Amy Lew
- Department of Chemistry, University of California, Irvine, California 92697, USA
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